Hi Andreas I don't think you got a reply to this. I've had a trawl through the messages to the EMBOSS lists ... perhaps some of the following will help (I'm no expert on cygwin) ? A port of EMBOSS 3 to windows will be made available soonish - so you'll never need to use cygwin again.
Cheers Jon 1. Apply all the fixes from: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ 2. Update cygwin Problems can arise from using older versions of cygwin, or selective ("pick and choose") installations of cygwin. Download a new, completely fresh copy of cygwin (the cygwin updating mechanism has proved unsatisfactory) and accept the default packages; best to get a pretty complete set of cygwin packages. If you decide to install a fresh copy then be sure to delete any cygwin registry entries after deleting the cygwin directory: see (1) DELETING CYGWIN below (email emboss-bug if the registry fixing script cygtidy.reg is not available on the website). Your cygwin installation directory should be around 1.5 - 2Gb in size. 3. Read the instructions on the web, but see the corrections (1) to that text, which haven't made it onto the website yet: http://emboss.sourceforge.net/download/cygwin.html The instructions imply that --without-x is essential, whereas X windows works fine as long as you've installed it under cygwin. It also suggests using CFLAGS=-s to the configure, presumably to strip the binaries. This should not be required as the latest cygwin distributions automatically strip the binaries. (1) CORRECTIONS / ADDITIONS 1) install cygwin (http://www.cygwin.com). That's surely possible to compile without it, but it's making everything easier. You'll have to install the base part plus the devel/make and devel/gcc packages. Before installing, see the first line of 2). Then you'll have a linux-like command-line with tools like gcc and make. The paths are then made according to the place where you installed cygwin (ex: c\cygwin becomes /). Notes from the EMBOSS developers: We recommend doing a full cygwin installation or problems may arise with creating the DLLs. 3) quit and restart the cygwin bash (you'll start in your "FirstName_LastName" directory, you can delete "FirstName LastName"), download the EMBOSS package and cd to the place where you uncompressed it. Follow the usual procedure: ./configure --without-x CFLAGS=-s make make install --without-x because at one point the X11 library is required (even if useless) and without this flag the compilation would stop. CFLAGS=-s to make the binaries smaller. Notes from the EMBOSS developers: If you have done a reasonably full cygwin installation then you can leave out the --without-x switch. X will work perfectly well if installed. Also, with later cygwin installations, you can omit the CFLAGS=-s switch. We also recommend providing a prefix switch to install EMBOSS in a specified location. The configuration then becomes: ./configure --prefix=/usr/local/emboss make make install After installation make sure that /usr/local/emboss/bin is in your PATH. DELETING CYGWIN To delete cygwin you should drag your cygwin installation directory to the recycle bin. Then delete any cygwin entries from the 'start' menu. You should then download the file cygtidy.reg and double-click it to remove any cygwin registry entries. > Hi, I download Emboss package and tried to install it under cygwin. I > keep getting the error message cc1.exe - Entry Point not found The > procedure entry point_impure_ptr could not be located in the dynamic > link library cygwin1.dll when I try to run the: "./configure --without-x > CFLAGS=-s" command. I am using: > cygwin: 1.5.19-4 > gcc: 3.4.4-1 > It seems that my cygwin installation might not have worked, i.e. there > is an incompatibility issue between GCC and Cygwin. Any suggestions? > Thanks a lot > Andreas > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
